Systems, apparatuses, and methods for managing buffers in a neural network implementation with heterogeneous memory are disclosed. A system includes a neural network coupled to a first memory and a second memory. The first memory is a relatively low-capacity, high-bandwidth memory while the second memory is a relatively high-capacity, low-bandwidth memory. During a forward propagation pass of the neural network, a run-time manager monitors the usage of the buffers for the various layers of the neural network. During a backward propagation pass of the neural network, the run-time manager determines how to move the buffers between the first and second memories based on the monitored buffer usage during the forward propagation pass. As a result, the run-time manager is able to reduce memory access latency for the layers of the neural network during the backward propagation pass.